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apbs_cgi.py
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apbs_cgi.py
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#!@WHICHPYTHON@
"""
APBS input form [fill in later]
"""
__date__ = "22 June 2007"
__author__ = "Samir Unni"
__version__ = "0.0.1"
import string, sys, os, time, errno, shutil, tempfile, urllib, copy, pickle, glob
#sys.path.append("/home/samir/public_html/pdb2pqr")
import src
import cgi, cgitb
import locale
from sys import stdout, stderr, stdin
from src.aconf import *
from src.server import setID
#from initVars import *
#from generateForm import generateForm
#from apbsInputMake import *
#from apbsExec import apbsExec
#from apbsExec import apbsOpalExec
from sgmllib import SGMLParser
from src.utilities import (getTrackingScriptString,
getEventTrackingString,
startLogFile,
resetLogFile)
def apbsOpalExec(logTime, form, apbsOptions):
sys.path.append(os.path.dirname(APBS_LOCATION))
from ApbsClient import execApbs, initRemoteVars, enoughMemory
#style = "%spdb2pqr.css" # HARDCODED
#apbsLog = "apbs_runtime_output.log"
#apbsErrs = "apbs_errors.log"
# Copies PQR file to temporary directory
pqrFileName = form["pdb2pqrid"].value + '.pqr'
#shutil.copyfile('../pdb2pqr/tmp/%s' % pqrFileName, './tmp/%s/%s' % (logTime, pqrFileName))
# Removes water from molecule if requested by the user
if form.has_key("removewater"):
if form["removewater"].value == "on":
os.chdir('./tmp/%s' % logTime)
inpath = pqrFileName
infile = open(inpath, "r")
outpath = inpath[:-4] + '-nowater' + inpath[-4:]
outfile = open(outpath, "w")
newinpath = inpath[:-4] + '-water' + inpath[-4:]
newoutpath = inpath
while 1:
line = infile.readline()
if line == '':
break
if "WAT" in line:
pass
elif "HOH" in line:
pass
else:
outfile.write(line)
infile.close()
outfile.close()
shutil.move(inpath, newinpath)
shutil.move(outpath, newoutpath)
os.chdir('../../')
#argv=[os.path.abspath("tmp/%s/%s.in") % (logTime, "apbsinput")] # HARDCODED??
argv=[os.path.abspath("%s%s%s/apbsinput.in" % (INSTALLDIR, TMPDIR, logTime))]
vars={'service_url' : APBS_OPAL_URL}
# Check for enough memory
if(not enoughMemory(argv[-1])):
return 'notenoughmem'
appServicePortArray = execApbs(vars=vars, argv=argv)
# if the version number doesn't match, execApbs returns False
if(appServicePortArray == False):
return False
appServicePort = appServicePortArray[0]
#aspFile = open('./tmp/%s/%s-asp' % (logTime, logTime),'w')
#pickle.dump(appServicePort, aspFile)
#aspFile.close()
resp = appServicePortArray[1]
return resp._jobID
def apbsExec(logTime, form, apbsOptions):
tempPage = "results.html"
# Temporary index.py html page - refreshes in 30 seconds
#apbsLog = "apbs_runtime_output.log"
#apbsErrs = "apbs_errors.log"
# Copies PQR file to temporary directory
pqrFileName = form["pdb2pqrid"].value + '.pqr'
#shutil.copyfile('../pdb2pqr/tmp/%s' % pqrFileName, './tmp/%s/%s' % (logTime, pqrFileName))
# Removes water from molecule if requested by the user
try:
if form["removewater"].value == "on":
os.chdir('./tmp/%s' % logTime)
inpath = pqrFileName
infile = open(inpath, "r")
outpath = inpath[:-4] + '-nowater' + inpath[-4:]
outfile = open(outpath, "w")
newinpath = inpath[:-4] + '-water' + inpath[-4:]
newoutpath = inpath
while 1:
line = infile.readline()
if line == '':
break
if "WAT" in line:
pass
elif "HOH" in line:
pass
else:
outfile.write(line)
infile.close()
outfile.close()
shutil.move(inpath, newinpath)
shutil.move(outpath, newoutpath)
os.chdir('../../')
except KeyError:
pass
pid = os.fork()
if pid:
print redirector(logTime)
sys.exit()
else:
currentdir = os.getcwd()
os.chdir("/")
os.setsid()
os.umask(0)
os.chdir(currentdir)
os.close(1)
os.close(2)
#os.chdir('./tmp/%s' % logTime)
os.chdir('%s%s%s' % (INSTALLDIR, TMPDIR, logTime))
# LAUNCHING APBS HERE
startLogFile(logTime, 'apbs_status', "running\n")
# statusfile = open('%s%s%s/apbs_status' % (INSTALLDIR, TMPDIR, logTime),'w')
# statusfile.write("running\n")
# statusfile.close()
apbs_stdin, apbs_stdout, apbs_stderr = os.popen3('%s apbsinput.in' % APBS_LOCATION)
startLogFile(logTime, 'apbs_stdout.txt', apbs_stdout.read())
# stdoutFile=open('%s%s%s/apbs_stdout.txt' % (INSTALLDIR, TMPDIR, logTime), 'w')
# stdoutFile.write(apbs_stdout.read())
# stdoutFile.close()
startLogFile(logTime, 'apbs_stderr.txt', apbs_stderr.read())
# stderrFile=open('%s%s%s/apbs_stderr.txt' % (INSTALLDIR, TMPDIR, logTime), 'w')
# stderrFile.write(apbs_stderr.read())
# stderrFile.close()
startLogFile(logTime, 'apbs_end_time', str(time.time()))
# endtimefile=open('%s%s%s/apbs_end_time' % (INSTALLDIR, TMPDIR, logTime), 'w')
# endtimefile.write(str(time.time()))
# endtimefile.close()
jobDir = '%s%s%s/' % (INSTALLDIR, TMPDIR, logTime)
statusStr = "complete\n"
statusStr += jobDir + 'apbsinput.in\n'
statusStr += jobDir + '%s.pqr\n' % logTime
statusStr += jobDir + 'io.mc\n'
for filename in glob.glob(jobDir+"%s-*.dx" % logTime):
statusStr += (filename+"\n")
statusStr += jobDir + 'apbs_stdout.txt\n'
statusStr += jobDir + 'apbs_stderr.txt\n'
startLogFile(logTime, 'apbs_status', statusStr)
# statusfile=open('%s%s%s/apbs_status' % (INSTALLDIR, TMPDIR, logTime),'w')
# statusfile.write("complete\n")
# statusfile.write("%s%s%s/apbsinput.in\n" % (INSTALLDIR, TMPDIR, logTime))
# statusfile.write("%s%s%s/%s.pqr\n" % (INSTALLDIR, TMPDIR, logTime, logTime))
# statusfile.write("%s%s%s/io.mc\n" % (INSTALLDIR, TMPDIR, logTime))
# for filename in glob.glob("%s%s%s/%s-*.dx" % (INSTALLDIR, TMPDIR, logTime, logTime)):
# statusfile.write(filename+"\n")
# statusfile.write("%s%s%s/apbs_stdout.txt\n" % (INSTALLDIR, TMPDIR, logTime))
# statusfile.write("%s%s%s/apbs_stderr.txt\n" % (INSTALLDIR, TMPDIR, logTime))
# statusfile.close()
sys.exit()
def generateForm(file, initVars, pdb2pqrID, type):
"""CGI form generation code"""
cgifile = "apbs_cgi.cgi"
cginame = "thisform"
file.write("""<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<title>APBS input</title>
<link href="pdb2pqr.css" type="text/css" rel="stylesheet" />
<script type=\"text/javascript\">
function showHide(elemShow, elemHide) {
document.getElementById(elemHide).style.display = 'none';
//document.getElementById(elemShow).style.display = 'block';
//document.getElementById(elemShow).style.visibility= 'visible';
document.getElementById(elemShow).style.display = '';
}
function toggle(element) {
if(document.getElementById(element).style.display == 'none') {
document.getElementById(element).style.display = '';
}
else {
document.getElementById(element).style.display = 'none';
}
}
function getElementsByClass(searchClass,node,tag) {
var classElements = new Array();
if ( node == null )
node = document;
if ( tag == null )
tag = '*';
var els = node.getElementsByTagName(tag);
var elsLen = els.length;
//var pattern = new RegExp("(^|\\\\\\\\s)"+searchClass+"(\\\\\\\\s|$)");
for (i = 0, j = 0; i < elsLen; i++) {
//if ( pattern.test(els[i].className) ) {
if( els[i].className.indexOf(searchClass) != -1) {
classElements[j] = els[i];
j++;
}
}
return classElements;
}
function disableCalcType(calcTypeToDisable) {
//var elements = getElementsByClass(calcTypeToDisable, null, 'div');
var elements = getElementsByClass(calcTypeToDisable);
for(var i=0; i<elements.length; i++) {
elements[i].style.display = 'none';
}
}
function showCalcType(calcType) {
//var calcTypesToDisable = ['mg-auto','mg-para','mg-manual','fe-manual','mg-dummy'];
var calcTypesToDisable = ['mg-auto','mg-para','mg-manual','fe-manual','mg-dummy'];
for(var i=0; i<calcTypesToDisable.length; i++) {
if(calcTypesToDisable[i]!=calcType) {
disableCalcType(calcTypesToDisable[i]);
}
}
//var elements = getElementsByClass(calcType, null, 'div');
var elements = getElementsByClass(calcType);
for(var i=0; i<elements.length; i++) {
//elements[i].style.display = 'block';
elements[i].style.display = '';
//elements[i].style.visibility = 'visible';
}
}
function findCheckedCalc() {
for(var i=0; i<document.%s.type.length; i++) {
if(document.%s.type[i].checked) {
type = document.%s.type[i];
return type;
}
}
}
function configInitCheckedCalc() {
showCalcType('%s');
}
function executeOnPageLoad(myfunc) {
if(window.addEventListener) {
window.addEventListener('load', myfunc, false);
}
else if(window.attachEvent) {
window.attachEvent('onload', myfunc);
}
}
executeOnPageLoad(configInitCheckedCalc);
</script>
</head>
<body>
<!-- ... body of document ... -->
<h2>APBS web solver</h2>
""" % (cginame, cginame, cginame, initVars['calculationType'])) # hardcoded css link
file.write("<h3>Calculation on <a href=\"tmp/%s/%s\" target=\"_blank\">%s</a> with default values provided by PDB2PQR:</h3><br />\n" % (pdb2pqrID, initVars['pqrname'],initVars['pdbID']))
# Write out the form element
print "<form action=\"%s\" method=\"post\" enctype=\"multipart/form-data\" name=\"%s\" id=\"%s\">" % (cgifile, cginame, cginame)
print "<input type=\"submit\" value=\"Launch\"/><br /><br />"
print """
If you prefer to run APBS with custom values, click here:
<input type=\"checkbox\" name=\"customvalues\" onClick=\"toggle(\'params\');"/>
<br /><br />
<div id=\"params\" style=\"display:none\">
Please specify the type of calculation (all parameters for the specified calculation must be fullfilled, unless indicated otherwise):
<br />
"""
print "<input type=\"radio\" name=\"type\" value=\"mg-auto\" onClick=\"showCalcType(\'mg-auto\');\"",
if initVars['calculationType'] == "mg-auto":
print " checked=\"checked\"",
print "/> Automatically-configured sequential focusing multigrid calculation <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#Automatic_sequential_focusing_multigrid_calculation_.28mg-auto.29\" target=\"_blank\"><font title=\"mg-auto\">(<span class=\"tooltip\">?</span>)</font></a>"
print "<br />"
print "<input type=\"radio\" name=\"type\" value=\"mg-para\" onClick=\"showCalcType(\'mg-para\');\"",
if initVars['calculationType'] == "mg-para":
print " checked=\"checked\"",
#print "disabled=\"disabled\""
print """/> Automatically-configured parallel focusing multigrid calculation <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#Automatic_parallel_focusing_multigrid_calculation_.28mg-para.29\" target=\"_blank\"><font title=\"mg-para\">(<span class=\"tooltip\">?</span>)</font></a>"""
print "<br />"
print "<input type=\"radio\" name=\"type\" value=\"mg-manual\" onClick=\"showCalcType(\'mg-manual\');\"",
if initVars['calculationType'] == "mg-manual":
print " checked=\"checked\"",
#print "disabled=\"disabled\""
print """/> Manually-configured multigrid calculation <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#Manual_multigrid_calculation_.28mg-manual.29\" target=\"_blank\"><font title=\"mg-manual\">(<span class=\"tooltip\">?</span>)</font></a>"""
print "<br />"
print "<input type=\"radio\" name=\"type\" value=\"fe-manual\" onClick=\"showCalcType(\'fe-manual\');\"",
if initVars['calculationType'] == "fe-manual":
print " checked=\"checked\"",
#print "disabled=\"disabled\""
print """/> Manually-configured adaptive finite element calculation <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#Manual_adaptive_finite_element_calculation_.28fe-manual.29\" target=\"_blank\"><font title=\"fe-manual\">(<span class=\"tooltip\">?</span>)</font></a>"""
print "<br />"
print "<input type=\"radio\" name=\"type\" value=\"mg-dummy\" onClick=\"showCalcType(\'mg-dummy\');\"",
if initVars['calculationType'] == "mg-dummy":
print " checked=\"checked\"",
#print "disabled=\"disabled\""
print """/> Surface and charge distribution property calculations (does not require solution of the PBE) <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#Manual_non-numerical_calculations_.28mg-dummy.29\" target=\"_blank\"><font title=\"mg-dummy\">(<span class=\"tooltip\">?</span>)</font></a>"""
print "<ul><li><input type=\"checkbox\" name=\"removewater\" value=\"on\" checked=\"checked\"/> Remove water from calculations and visualizations</li></ul>"
print """
<div class=\"mg-auto mg-para mg-manual mg-dummy\">
<ul>"""
print """
<table class=\"apbs\" border=\"1\">
<tr>
<th></th>
<th>x-direction</th>
<th>y-direction</th>
<th>z-direction</th>
</tr>
<tbody class=\"mg-auto mg-para mg-manual mg-dummy\">
<tr>
<td>Number of grid points<br />per processor for grid-<br />based discretization <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#dime\" target=\"_blank\"><font title=\"dime\">(<span class=\"tooltip\">?</span>)</font></a></td>
<td><input type=\"text\" name=\"dimenx\" size=\"10\" maxlength=\"20\""""
if initVars.has_key('dime'):
print "value=\"%d\"" % initVars['dime'][0]
print "/></td>"
print "<td><input type=\"text\" name=\"dimeny\" size=\"10\" maxlength=\"20\""
if initVars.has_key('dime'):
print "value=\"%d\"" % initVars['dime'][1]
print "/></td>"
print "<td><input type=\"text\" name=\"dimenz\" size=\"10\" maxlength=\"20\""
if initVars.has_key('dime'):
print "value=\"%d\"" % initVars['dime'][2]
print "/></td></tr></tbody>"
# next row
print "<tbody class=\"mg-auto mg-para mg-dummy\">"
print "<tr>"
print "<td>Coarse mesh domain<br />lengths in a focusing<br />calculation <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#cglen\" target=\"_blank\"><font title=\"cglen\">(<span class=\"tooltip\">?</span>)</font></a></td>"
print "<td><input type=\"text\" name=\"cglenx\" size=\"10\" maxlength=\"20\""
if initVars.has_key('coarseGridLength'):
print "value=\"%g\"" % initVars['coarseGridLength'][0]
print "/>"
print "<td><input type=\"text\" name=\"cgleny\" size=\"10\" maxlength=\"20\""
if initVars.has_key('coarseGridLength'):
print "value=\"%g\"" % initVars['coarseGridLength'][1]
print "/>"
print "<td><input type=\"text\" name=\"cglenz\" size=\"10\" maxlength=\"20\""
if initVars.has_key('coarseGridLength'):
print "value=\"%g\"" % initVars['coarseGridLength'][2]
print "/></td></tr></tbody>"
# next row
print "<tbody class=\"mg-auto mg-para\">"
print "<tr>"
print "<td>Fine mesh domain<br />lengths in a focusing<br />calculation <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#fglen\" target=\"_blank\"><font title=\"fglen\">(<span class=\"tooltip\">?</span>)</font></a></td>"
print "<td><input type=\"text\" name=\"fglenx\" size=\"10\" maxlength=\"20\""
if initVars.has_key('fineGridLength'):
print "value=\"%g\"" % initVars['fineGridLength'][0]
print "/>"
print "<td><input type=\"text\" name=\"fgleny\" size=\"10\" maxlength=\"20\""
if initVars.has_key('fineGridLength'):
print "value=\"%g\"" % initVars['fineGridLength'][1]
print "/>"
print "<td><input type=\"text\" name=\"fglenz\" size=\"10\" maxlength=\"20\""
if initVars.has_key('fineGridLength'):
print "value=\"%g\"" % initVars['fineGridLength'][2]
print "/></td></tr></tbody>"
# next row
print "<tbody class=\"mg-para\">"
print "<tr>"
print "<td>Number of proces-<br />sors in a parallel<br />focusing calculation <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#pdime\" target=\"_blank\"><font title=\"pdime\">(<span class=\"tooltip\">?</span>)</font></a></td>"
print "<td><input type=\"text\" name=\"pdimex\" size=\"10\" maxlength=\"20\""
if initVars.has_key('pdime'):
print "value=\"%g\"" % initVars['pdime'][0]
print "/>"
print "<td><input type=\"text\" name=\"pdimey\" size=\"10\" maxlength=\"20\""
if initVars.has_key('pdime'):
print "value=\"%g\"" % initVars['pdime'][1]
print "/>"
print "<td><input type=\"text\" name=\"pdimez\" size=\"10\" maxlength=\"20\""
if initVars.has_key('pdime'):
print "value=\"%g\"" % initVars['pdime'][2]
print "/></td></tr></tbody>"
# next row
print "<tbody class=\"mg-manual\">"
print "<tr>"
print "<td>Mesh domain<br />lengths <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#glen\" target=\"_blank\"><font title=\"glen\">(<span class=\"tooltip\">?</span>)</font></a></td>"
print "<td><input type=\"text\" name=\"glenx\" size=\"10\" maxlength=\"20\""
if initVars.has_key('glen'):
print "value=\"%g\"" % initVars['glen'][0]
print "/>"
print "<td><input type=\"text\" name=\"gleny\" size=\"10\" maxlength=\"20\""
if initVars.has_key('glen'):
print "value=\"%g\"" % initVars['glen'][1]
print "/>"
print "<td><input type=\"text\" name=\"glenz\" size=\"10\" maxlength=\"20\""
if initVars.has_key('glen'):
print "value=\"%g\"" % initVars['glen'][2]
print "/></td></tr></tbody>"
print "</table></div></ul>"
print """ <div class=\"mg-para\"><ul>
<li>Amount of overlap to include between the individual processors' meshes <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#ofrac\" target=\"_blank\"><font title=\"ofrac\">(<span class=\"tooltip\">?</span>)</font></a>:"""
print "<input type=\"text\" name=\"ofrac\" size=\"10\" maxlength=\"20\""
if initVars.has_key('processorMeshOverlap'):
print "value=\"%f\"" % initVars['processorMeshOverlap']
print "/></li><br />"
print "<li><input type=\"checkbox\" name=\"asyncflag\" onClick=toggle(\"async\") "
if initVars['asyncflag']:
print " checked=\"checked\""
print """/> Perform the tasks in a parallel run asynchronously <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#async\" target=\"_blank\"><font title=\"asyncflag\">(<span class=\"tooltip\">?</span>)</font></a></li>"""
print "<blockquote>"
print "<div id=\"async\" style=\"display:none\">"
print "<li>Rank for a processor to masquerade as <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#async\" target=\"_blank\"><font title=\"async\">(<span class=\"tooltip\">?</span>)</font></a>:"
print "<input type=\"text\" name=\"async\" size=\"10\" maxlength=\"20\""
if initVars.has_key('async'):
print " value=\"%i\"" % initVars['async']
print "/></li>"
print "</blockquote>"
print "</li></ul></div>"
print "<div class=\"mg-manual mg-dummy\">"
print "<ul><li>Depth of the multilevel hierarchy used in the multigrid solver <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#nlev\" target=\"_blank\"><font title=\"nlev\">(<span class=\"tooltip\">?</span>)</font></a>:"
print "<input type=\"text\" name=\"nlev\" size=\"10\" maxlength=\"20\""
if initVars.has_key('nlev'):
print " value=\"%i\"" % initVars['nlev']
print "/></li></ul></div>"
print """ <div class=\"mg-manual mg-dummy\"><ul>
<li>Center of the grid <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#gcent\" target=\"_blank\"><font title=\"gcent\">(<span class=\"tooltip\">?</span>)</font></a>:</li></ul>
<blockquote><ul><li>"""
print "<input type=\"radio\" name=\"gcent\" value=\"mol\" onClick=\"showHide(\'gcentmol\',\'gcentcoord\');\""
if initVars['gridCenterMethod'] == "molecule":
print "checked=\"checked\""
print "/> Center the grid on a molecule.</li></ul>"
print "<div id=\"gcentmol\""
if initVars['gridCenterMethod'] != "molecule":
print " style=\"display: none;\""
print"""><blockquote>
<ul>
<li>Enter molecule ID:"""
print "<input type=\"text\" name=\"gcentid\" size=\"10\" maxlength=\"20\""
if initVars['gridCenterMethod'] == "molecule" and initVars.has_key('gridCenterMoleculeID'):
print "value=\"%d\"" % initVars['gridCenterMoleculeID']
print "/>"
print """
</li>
</ul>
</blockquote></div>
"""
print "<ul><li><input type=\"radio\" name=\"gcent\" value=\"coord\" onClick=\"showHide(\'gcentcoord\',\'gcentmol\');\""
if initVars['gridCenterMethod'] == "coordinate":
print "checked"
print "/> Manually enter coordinates for center of grid:</li></ul>"
print "<div id=\"gcentcoord\""
if initVars['gridCenterMethod'] != "coordinate":
print "style=\"display: none;\""
print """><blockquote>
<ul>
<li>"""
print "x-coordinate: <input type=\"text\" name=\"gxcent\" size=\"10\" maxlength=\"20\""
if initVars.has_key('gridCenter'):
print "value=\"%d\"" % initVars['gridCenter'][0]
print "/>"
print """
</li>
<li>"""
print "y-coordinate: <input type=\"text\" name=\"gycent\" size=\"10\" maxlength=\"20\""
if initVars.has_key('gridCenter'):
print "value=\"%d\"" % initVars['gridCenter'][1]
print "/>"
print """
</li>
<li>"""
print "z-coordinate: <input type=\"text\" name=\"gzcent\" size=\"10\" maxlength=\"20\""
if initVars.has_key('gridCenter'):
print "value=\"%d\"" % initVars['gridCenter'][2]
print "/>"
print "</li></ul></blockquote></div>"
print "</blockquote>"
print "</div>"
print """
<div class=\"mg-auto mg-para\"><ul>
<li>Center of the coarse grid <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#cgcent\" target=\"_blank\"><font title=\"cgcent\">(<span class=\"tooltip\">?</span>)</font></a>:</li></ul>
<blockquote><ul><li>"""
print "<input type=\"radio\" name=\"cgcent\" value=\"mol\" onClick=\"showHide(\'cgcentmol\',\'cgcentcoord\');\""
if initVars['coarseGridCenterMethod'] == "molecule":
print "checked=\"checked\""
print "/> Center the grid on a molecule.</li></ul>"
print "<div id=\"cgcentmol\""
if initVars['coarseGridCenterMethod'] != "molecule":
print " style=\"display: none;\""
print"""><blockquote>
<ul>
<li>Enter molecule ID:"""
print "<input type=\"text\" name=\"cgcentid\" size=\"10\" maxlength=\"20\""
if initVars['coarseGridCenterMethod'] == "molecule" and initVars.has_key('coarseGridCenterMoleculeID'):
print "value=\"%d\"" % initVars['coarseGridCenterMoleculeID']
print "/>"
print """
</li>
</ul>
</blockquote>
</div>
"""
print "<ul><li><input type=\"radio\" name=\"cgcent\" value=\"coord\" onClick=\"showHide(\'cgcentcoord\',\'cgcentmol\');\""
if initVars['coarseGridCenterMethod'] == "coordinate":
print "checked"
print "/> Manually enter coordinates for center of grid:</li></ul>"
print "<div id=\"cgcentcoord\""
if initVars['coarseGridCenterMethod'] != "coordinate":
print "style=\"display: none;\""
print """><blockquote>
<ul>
<li>"""
print "x-coordinate: <input type=\"text\" name=\"cgxcent\" size=\"10\" maxlength=\"20\""
if initVars.has_key('coarseGridCenter'):
print "value=\"%d\"" % initVars['coarseGridCenter'][0]
print "/>"
print """
</li>
<li>"""
print "y-coordinate: <input type=\"text\" name=\"cgycent\" size=\"10\" maxlength=\"20\""
if initVars.has_key('coarseGridCenter'):
print "value=\"%d\"" % initVars['coarseGridCenter'][1]
print "/>"
print """
</li>
<li>"""
print "z-coordinate: <input type=\"text\" name=\"cgzcent\" size=\"10\" maxlength=\"20\""
if initVars.has_key('coarseGridCenter'):
print "value=\"%d\"" % initVars['coarseGridCenter'][2]
print "/>"
print """</li></ul></blockquote>
</blockquote>"""
#"""</div>"""
print """
<ul>
<li>Center of the fine grid <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#fgcent\" target=\"_blank\"><font title=\"fgcent\">(<span class=\"tooltip\">?</span>)</font></a>:</li></ul>
<blockquote>
<ul><li>"""
print "<input type=\"radio\" name=\"fgcent\" value=\"mol\" onClick=\"showHide(\'fgcentmol\',\'fgcentcoord\');\""
if initVars['fineGridCenterMethod'] == "molecule":
print "checked=\"checked\""
print "/> Center the grid on a molecule.</li></ul>"
print "<div id=\"fgcentmol\""
if initVars['fineGridCenterMethod'] != "molecule":
print "style=\"display: none\""
print """
><blockquote>
<ul>
<li>Enter molecule ID:"""
print "<input type=\"text\" name=\"fgcentid\" size=\"10\" maxlength=\"20\""
if initVars['fineGridCenterMethod'] == "molecule" and initVars.has_key('fineGridCenterMoleculeID'):
print "value=\"%d\"" % initVars['fineGridCenterMoleculeID']
print "/>"
print """
</li>
</ul>
</blockquote></div>"""
print "<ul><li><input type=\"radio\" name=\"fgcent\" value=\"coord\" onClick=\"showHide(\'fgcentcoord\',\'fgcentmol\');\""
if initVars['fineGridCenterMethod'] == "coordinate":
print "checked"
print "/> Manually enter coordinates for the center of the grid.</li></ul>"
print "<div id=\"fgcentcoord\""
if initVars['fineGridCenterMethod'] != "coordinate":
print "style=\"display: none;\""
print """
><blockquote>
<ul>
<li>"""
print "x-coordinate: <input type=\"text\" name=\"fgxcent\" size=\"10\" maxlength=\"20\""
if initVars.has_key('fineGridCenter'):
print "value=\"%d\"" % initVars['fineGridCenter'][0]
print "/>"
print """
</li>
<li>"""
print "y-coordinate: <input type=\"text\" name=\"fgycent\" size=\"10\" maxlength=\"20\""
if initVars.has_key('fineGridCenter'):
print "value=\"%d\"" % initVars['fineGridCenter'][1]
print "/>"
print """
</li>
<li>"""
print "z-coordinate: <input type=\"text\" name=\"fgzcent\" size=\"10\" maxlength=\"20\""
if initVars.has_key('fineGridCenter'):
print "value=\"%d\"" % initVars['fineGridCenter'][2]
print "/>"
print """
</li>
</ul>
</blockquote>
</blockquote>
</div>"""#</div>"""
#print """<ul>
# <div class=\"mg-para mg-manual fe-manual mg-dummy\""""
#print """>
# <li>Molecule for which the PBE is to be solved <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#mol\" target=\"_blank\"><font title=\"mol\">(<span class=\"tooltip\">?</span>)</font></a>:"""
#print "<input type=\"text\" name=\"mol\" size=\"10\" maxlength=\"20\""
#if initVars.molecule != None:
# print "value=\"%d\"" % initVars.molecule
#print "/></li></div>"
#print """</ul>
print """ <ul>
<li>Type of PBE to be solved:</li></ul>"""
print """<blockquote>
<ul>"""
print "<li><input type=\"radio\" name=\"solvetype\" value=\"lpbe\""
if initVars['solveType'] == "linearized":
print "checked=\"checked\""
print "/> Linearized <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#lpbe\" target=\"_blank\"><font title=\"lpbe\">(<span class=\"tooltip\">?</span>)</font></a></li>"
print "<li><input type=\"radio\" name=\"solvetype\" value=\"npbe\""
if initVars['solveType'] == "nonlinearized":
print "checked=\"checked\""
print "/> Nonlinearized <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#npbe\" target=\"_blank\"><font title=\"npbe\">(<span class=\"tooltip\">?</span>)</font></a></li>"
print "<div class=\"fe-manual\""
#if initVars.defaultCalcType != "fe-manual":
# print " style=\"display: none;\""
print "><li><input type=\"radio\" name=\"solvetype\" value=\"lrpbe\""
if initVars['solveType'] == "linearized regularized":
print "checked=\"checked\""
print "/> Linearized (regularized) <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#lrpbe\" target=\"_blank\"><font title=\"lrpbe\">(<span class=\"tooltip\">?</span>)</font></a></li>"
print "<li><input type=\"radio\" name=\"solvetype\" value=\"nrpbe\""
if initVars['solveType'] == "nonlinearized regularized":
print "checked=\"checked\""
print "/> Nonlinearized (regularized) <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#nrpbe\" target=\"_blank\"><font title=\"nrpbe\">(<span class=\"tooltip\">?</span>)</font></a></li></div>"
print """</ul>
</blockquote>"""
print " <ul><li>Boundary condition definition <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#bcfl\" target=\"_blank\"><font title=\"bcfl\">(<span class=\"tooltip\">?</span>)</font></a>:</li></ul>"
print "<blockquote> <ul>"
print "<li><input type=\"radio\" name=\"bcfl\" value=\"zero\""
if initVars['boundaryConditions'] == "zero":
print "checked=\"checked\""
print "/> Zero <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#bcfl\" target=\"_blank\"><font title=\"zero\">(<span class=\"tooltip\">?</span>)</font></a></li>"
print "<li><input type=\"radio\" name=\"bcfl\" value=\"sdh\""
if initVars['boundaryConditions'] == "sdh":
print "checked=\"checked\""
print "/> Single Debye-Huckel <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#bcfl\" target=\"_blank\"><font title=\"sdh\">(<span class=\"tooltip\">?</span>)</font></a></li>"
print "<li><input type=\"radio\" name=\"bcfl\" value=\"mdh\""
if initVars['boundaryConditions'] == "mdh":
print "checked=\"checked\""
print "/> Multiple Debye-Huckel <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#bcfl\" target=\"_blank\"><font title=\"mdh\">(<span class=\"tooltip\">?</span>)</font></a></li>"
print "<li><input type=\"radio\" name=\"bcfl\" value=\"focus\""
if initVars['boundaryConditions'] == "focus":
print "checked=\"checked\""
print "/> Focusing <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#bcfl\" target=\"_blank\"><font title=\"focus\">(<span class=\"tooltip\">?</span>)</font></a></li>"
print "</ul></blockquote>"
print "<ul>"
print """ <li>Mobile ion species present in system (optional) <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#ion\" target=\"_blank\"><font title=\"ion\">(<span class=\"tooltip\">?</span>)</font></a>:</li></ul>"""
print """<ul>
<table class=\"apbs\" border=\"1\">
<tr>
<th></th>
<th>Mobile ion species<br />charge (in e<sub>c</sub>) <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#ion\" target=\"_blank\"><font title=\"charge\">(<span class=\"tooltip\">?</span>)</font></a></th>
<th>Mobile ion species<br />concentration (in M) <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#ion\" target=\"_blank\"><font title=\"conc\">(<span class=\"tooltip\">?</span>)</font></a></th>
<th>Mobile ion species<br />radius (in A) <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#ion\" target=\"_blank\"><font title=\"radius\">(<span class=\"tooltip\">?</span>)</font></a></th>
</tr>"""
# new row
for i in range(0,3):
print """<tr>
<td>Ion %d</td>
<td><input type=\"text\" name=\"charge%d\" size=\"10\" maxlength=\"20\"""" % ((i+1),i)
if initVars.has_key('mobileIonSpeciesCharge'):
print "value=\"%d\"" % initVars['mobileIonSpeciesCharge']
print "/></td>"
print """
<td><input type=\"text\" name=\"conc%d\" size=\"10\" maxlength=\"20\"""" % i
if initVars.has_key('mobileIonSpeciesConcentration'):
print "value=\"%d\"" % initVars['mobileIonSpeciesConcentration']
print "/></td>"
print """
<td><input type=\"text\" name=\"radius%d\" size=\"10\" maxlength=\"20\"""" % i
if initVars.has_key('mobileIonSpeciesRadius'):
print "value=\"%d\"" % initVars['mobileIonSpeciesRadius']
print "/></td>"
print "</tr></table></ul>"
#print """<blockquote><ul>
# <li>Mobile ion species charge (in e<sub>c</sub>) <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#ion\" target=\"_blank\"><font title=\"charge\">(<span class=\"tooltip\">?</span>)</font></a>: """
#print "<input type=\"text\" name=\"charge\" size=\"10\" maxlength=\"20\""
#if initVars.defaultMobileIonSpeciesCharge != None:
# print "value=\"%d\"" % initVars.defaultMobileIonSpeciesCharge
#print "/></li>"
#
#print " <li>Mobile ion species concentration (in M) <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#ion\" target=\"_blank\"><font title=\"conc\">(<span class=\"tooltip\">?</span>)</font></a>:"
#
#print "<input type=\"text\" name=\"conc\" size=\"10\" maxlength=\"20\""
#if initVars.defaultMobileIonSpeciesConcentration != None:
# print "value=\"%d\"" % initVars.defaultMobileIonSpeciesConcentration
#print "/></li>"
#print " <li>Mobile ion species radius (in A) <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#ion\" target=\"_blank\"><font title=\"radius\">(<span class=\"tooltip\">?</span>)</font></a>:"
#
#print "<input type=\"text\" name=\"radius\" size=\"10\" maxlength=\"20\""
#if initVars.defaultMobileIonSpeciesRadius != None:
# print "value=\"%d\"" % initVars.defaultMobileIonSpeciesRadius
#print "/></li>"
#print "</ul></blockquote>"
print " <ul><li>Biomolecular dielectric constant <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#pdie\" target=\"_blank\"><font title=\"pdie\">(<span class=\"tooltip\">?</span>)</font></a>:"
print "<input type=\"text\" name=\"pdie\" size=\"10\" maxlength=\"20\""
if initVars.has_key('biomolecularDielectricConstant'):
print "value=\"%g\"" % initVars['biomolecularDielectricConstant']
print "/>"
print """ </li>
</ul>"""
print " <ul><li>Dielectric constant of solvent <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#sdie\" target=\"_blank\"><font title=\"sdie\">(<span class=\"tooltip\">?</span>)</font></a>:"
print " <input type=\"text\" name=\"sdie\" size=\"10\" maxlength=\"20\""
if initVars.has_key('dielectricSolventConstant'):
print "value=\"%g\"" % initVars['dielectricSolventConstant']
print """/></li>
</ul>
<ul>
<li>Method by which the biomolecular point charges are mapped onto the grid <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#chgm\" target=\"_blank\"><font title=\"chgm\">(<span class=\"tooltip\">?</span>)</font></a>:</li></ul>"""
print "<blockquote><ul>"
print "<li><input type=\"radio\" name=\"chgm\" value=\"spl0\""
if initVars.has_key('biomolecularPointChargeMapMethod') and initVars['biomolecularPointChargeMapMethod'] == "spl0":
print "checked"
print "/> Traditional trilinear interpolation <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#chgm\" target=\"_blank\"><font title=\"spl0\">(<span class=\"tooltip\">?</span>)</font></a></li>"
print "<li><input type=\"radio\" name=\"chgm\" value=\"spl2\""
if initVars.has_key('biomolecularPointChargeMapMethod') and initVars['biomolecularPointChargeMapMethod'] == "spl2":
print "checked=\"checked\""
print "/> Cubic B-spline discretization <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#chgm\" target=\"_blank\"><font title=\"spl2\">(<span class=\"tooltip\">?</span>)</font></a></li>"
print "<li><input type=\"radio\" name=\"chgm\" value=\"spl4\""
if initVars.has_key('biomolecularPointChargeMapMethod') and initVars['biomolecularPointChargeMapMethod'] == "spl4":
print "checked"
print "/> Quintic B-spline discretization <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#chgm\" target=\"_blank\"><font title=\"spl4\">(<span class=\"tooltip\">?</span>)</a></font></li>"
print "</ul></blockquote>"
print " <ul><li>Number of grid points per square-angstrom to use in surface constructions <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#sdens\" target=\"_blank\"><font title=\"sdens\">(<span class=\"tooltip\">?</span>)</font></a>:"
print "<input type=\"text\" name=\"sdens\" size=\"10\" maxlength=\"20\""
if initVars.has_key('surfaceConstructionResolution'):
print "value=\"%g\"" % initVars['surfaceConstructionResolution']
print """ /></li></ul>
<ul><li>Model to use to construct the dielectric ion-accessibility coefficients <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#srfm\" target=\"_blank\"><font title=\"srfm\">(<span class=\"tooltip\">?</span>)</font></a>:</li></ul>"""
print "<blockquote> <ul>"
print "<li><input type=\"radio\" name=\"srfm\" value=\"mol\""
if initVars.has_key('dielectricIonAccessibilityModel') and initVars['dielectricIonAccessibilityModel'] == "mol":
print "checked=\"checked\""
print "/> Dielectric coefficient is defined based on a molecular surface definition; ion-accessibility coefficient is defined by an \"inflated\" van der Waals model <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#srfm\" target=\"_blank\"><font title=\"mol\">(<span class=\"tooltip\">?</span>)</font></a>.</li>"
print "<li><input type=\"radio\" name=\"srfm\" value=\"smol\""
if initVars.has_key('dielectricIonAccessibilityModel') and initVars['dielectricIonAccessibilityModel'] == "smol":
print "checked=\"checked\""
print "/> Dielectric and ion-accessiblity coefficients are defined as above, but then are then \"smoothed\" by a 9-point harmonic averaging to somewhat reduce sensitivity to the grid setup <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#srfm\" target=\"_blank\"><font title=\"smol\">(<span class=\"tooltip\">?</span>)</font></a>.</li>"
print "<li><input type=\"radio\" name=\"srfm\" value=\"spl2\""
if initVars.has_key('dielectricIonAccessibilityModel') and initVars['dielectricIonAccessibilityModel'] == "spl2":
print "checked=\"checked\""
print "/> Dielectric and ion-accessibility coefficients are defined by a cubic-spline surface <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#srfm\" target=\"_blank\"><font title=\"spl2\">(<span class=\"tooltip\">?</span>)</font></a>.</li>"
print "<li><input type=\"radio\" name=\"srfm\" value=\"spl4\""
if initVars.has_key('dielectricIonAccessibilityModel') and initVars['dielectricIonAccessibilityModel'] == "spl4":
print "checked=\"checked\""
print "/> Dielectric and ion-accessibility coefficients are defined by a 7th order polynomial <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#srfm\" target=\"_blank\"><font title=\"spl4\">(<span class=\"tooltip\">?</span>)</font></a>.</li>"
print "</ul></blockquote>"
print " <ul><li>Radius of the solvent molecules <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#srad\" target=\"_blank\"><font title=\"srad\">(<span class=\"tooltip\">?</span>)</font></a>:"
print "<input type=\"text\" name=\"srad\" size=\"10\" maxlength=\"20\""
if initVars['solventRadius'] != None:
print "value=\"%g\"" % initVars['solventRadius']
print """/></li></ul>
<ul><li>Size of the support for spline-based surface definitions <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#swin\" target=\"_blank\"><font title=\"swin\">(<span class=\"tooltip\">?</span>)</font></a>:"""
print "<input type=\"text\" name=\"swin\" size=\"10\" maxlength=\"20\""
if initVars.has_key('surfaceDefSupportSize'):
print "value=\"%g\"" % initVars['surfaceDefSupportSize']
print """/></li></ul>
<ul><li>Temperature for PBE calculation (in K) <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#temp\" target=\"_blank\"><font title=\"temp\">(<span class=\"tooltip\">?</span>)</font></a>:"""
print "<input type=\"text\" name=\"temp\" size=\"10\" maxlength=\"20\""
if initVars.has_key('temperature'):
print "value=\"%g\"" % initVars['temperature']
print """/></li></ul>
<ul><li>Calculation of electrostatic energy from a PBE calculation <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#calcenergy\" target=\"_blank\"><font title=\"calcenergy\">(<span class=\"tooltip\">?</span>)</font></a>:</li></ul>"""
print "<blockquote><ul>"
print "<li><input type=\"radio\" name=\"calcenergy\" value=\"no\""
if initVars['calculationEnergy'] == "no":
print "checked"
print """/> Don\'t calculate any energies <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#calcenergy\" target=\"_blank\"><font title=\"no\">(<span class=\"tooltip\">?</span>)</font></a>.</li>"""
print "<li><input type=\"radio\" name=\"calcenergy\" value=\"total\""
if initVars['calculationEnergy'] == "total":
print "checked=\"checked\""
print """/> Calculate and return total electrostatic energy for the entire molecule <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#calcenergy\" target=\"_blank\"><font title=\"total\">(<span class=\"tooltip\">?</span>)</font></a>.</li>"""
print "<li><input type=\"radio\" name=\"calcenergy\" value=\"comps\""
if initVars['calculationEnergy'] == "comps":
print "checked=\"checked\""
print """/> Calculate and return total electrostatic energy for the entire molecule as well as electrostatic energy components for each atom <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#calcenergy\" target=\"_blank\"><font title=\"comps\">(<span class=\"tooltip\">?</span>)</font></a>.</li>
</ul></blockquote>
<ul><li>Calculation of electrostatic and apolar force outputs from a PBE calculation <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#calcforce\" target=\"_blank\"><font title=\"calcforce\">(<span class=\"tooltip\">?</span>)</font></a>:</li></ul>"""
print "<blockquote><ul>"
print "<li><input type=\"radio\" name=\"calcforce\" value=\"no\""
if initVars['calculationForce'] == "no":
print "checked=\"checked\""
print """/> Don\'t calculate any forces <a href=\"http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#calcforce\" target=\"_blank\"><font title=\"no\">(<span class=\"tooltip\">?</span>)</font></a>.</li>"""
print "<li><input type=\"radio\" name=\"calcforce\" value=\"total\""
if initVars['calculationForce'] == "total":
print "checked=\"checked\""